Endophytic bacterial community of grapevine leaves influenced by sampling date and phytoplasma infection process

BMC Microbiology

Piero A Bianco¹  Fabio Quaglino¹  Paola Casati¹  Daniela Bulgari¹ 

[1] Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, Università degli Studi, via Celoria 2, 20133 Milan, Italy

关键词: Microbial ecology;    LH-PCR;    Taxon-specific real-time PCR;    Recovery;    Flavescence dorée;   

Others  :  1140652
DOI  :  10.1186/1471-2180-14-198

 received in 2013-11-26, accepted in 2014-07-04,  发布年份 2014

【 摘 要 】

Background

Endophytic bacteria benefit host plant directly or indirectly, e.g. by biocontrol of the pathogens. Up to now, their interactions with the host and with other microorganisms are poorly understood. Consequently, a crucial step for improving the knowledge of those relationships is to determine if pathogens or plant growing season influence endophytic bacterial diversity and dynamic.

Results

Four healthy, four phytoplasma diseased and four recovered (symptomatic plants that spontaneously regain a healthy condition) grapevine plants were sampled monthly from June to October 2010 in a vineyard in north-western Italy. Metagenomic DNA was extracted from sterilized leaves and the endophytic bacterial community dynamic and diversity were analyzed by taxon specific real-time PCR, Length-Heterogeneity PCR and genus-specific PCR. These analyses revealed that both sampling date and phytoplasma infection influenced the endophytic bacterial composition. Interestingly, in June, when the plants are symptomless and the pathogen is undetectable (i) the endophytic bacterial community associated with diseased grapevines was different from those in the other sampling dates, when the phytoplasmas are detectable inside samples; (ii) the microbial community associated with recovered plants differs from that living inside healthy and diseased plants. Interestingly, LH-PCR database identified bacteria previously reported as biocontrol agents in the examined grapevines. Of these, Burkholderia, Methylobacterium and Pantoea dynamic was influenced by the phytoplasma infection process and seasonality.

Conclusion

Results indicated that endophytic bacterial community composition in grapevine is correlated to both phytoplasma infection and sampling date. For the first time, data underlined that, in diseased plants, the pathogen infection process can decrease the impact of seasonality on community dynamic. Moreover, based on experimental evidences, it was reasonable to hypothesize that after recovery the restructured microbial community could maintain the main structure between seasons.

【 授权许可】

   
2014 Bulgari et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

【 参考文献 】

• [1]Schulz B, Boyle C: What Are Endophytes?. Berlin: Springer-Verlang; 2006.
• [2]Sun L, Qiu F, Zhang X, Dai X, Dong X, Song W: Endophytic bacterial diversity in rice (Oryza sativa L.) roots estimated by 16S rDNA sequences analysis. Microb Ecol 2008, 55:415-424.
• [3]Ulrich K, Ulrich A, Ewald D: Diversity of endophytic bacterial communities in poplar grown under field condition. FEMS Microbiol Ecol 2008, 63:169-180.
• [4]Bulgari D, Casati P, Brusetti L, Quaglino F, Brasca M, Daffonchio D, Bianco PA: Endophytic bacterial diversity in grapevine (Vitis viniferaL.) leaves described by 16S rRNA gene sequence analysis and length heterogeneity-PCR. J Microbiol 2009, 47:393-401.
• [5]Bulgari D, Bozkurt AI, Casati P, Caglayan K, Quaglino F, Bianco PA: Endophytic bacterial community living in roots of healthy and ‘Candidatus Phytoplasma mali’-infected apple (Malusdomestica, Borkh.) trees. Antonie Van Leeuwenhoek 2012, 102:677-687.
• [6]McCully ME: Niches for bacterial endophytes in crop plants: a plant biologist’s view. Aust J Plant Physiol 2001, 28:983-990.
• [7]Compant S, Clément C, Sessitsch A: Plant growth promoting bacteria in the rhizo- and endosphere of plants. Their role, colonization, mechanisms involved and prospects for utilization. Soil Biol Biochem 2010, 42:669-678.
• [8]Lugtenberg B, Kamilova F: Plant-growth-promoting rhizobacteria. Annu Rev Microbiol 2009, 63:541-556.
• [9]Compant S, Duffy B, Nowak J, Clement C, Barka EA: Use of plant growth-promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action, and future prospects. Appl Environ Microbiol 2005, 71:4951-4959.
• [10]Lodewyckx C, Vangronsveld J, Porteous F, Moore ERB, Taghavi S, Mezgeay M, van der Lelie D: Endophytic bacteria and their potential applications. Crit Rev Plant Sci 2002, 21:583-606.
• [11]Trivedi P, Duan Y, Wang N: Huanglongbing, a systemic disease, restructures the bacterial community associated with citrus roots. Appl Environ Microbiol 2010, 76:3427-3436.
• [12]Trivedi P, He Z, Van Nostrand JD, Albrigo G, Zhou J, Wang N: Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere. ISME J 2012, 6:363-383.
• [13]Bulgari D, Casati P, Crepaldi P, Daffonchio D, Quaglino F, Brusetti L, Bianco PA: Restructuring of endophytic bacterial communities in grapevine yellows-diseased and recovered Vitis vinifera L. plants. Appl Environ Microbiol 2011, 77:5018-5022.
• [14]Ding T, Palmer MW, Melcher U: Community terminal restriction fragment length polymorphisms reveal insights into the diversity and dynamic of leaf endophytic bacteria. BMC Microbiol 2013, 13:1-11. BioMed Central Full Text
• [15]Quaglino F, Casati P, Bianco PA: Distinct rpsC single nucleotide polymorphism lineages of Flavescence Dorée subgroup 16SrV-D phytoplasma co-infect Vitis vinifera L. Folia Microbiol 2010, 55:251-257.
• [16]Belli G, Bianco PA, Conti M: Grapevine yellows in Italy: past, present and future. J Plant Pathol 2010, 92:303-326.
• [17]Durante G, Calvi M, Colombo A, Bianco PA, Casati P: Real-Time PCR Assay for Diagnosis of Flavescence Dorée (16Sr-V). 2009, 159-160. [Le Progrès Agricole et ViticoleHS]
• [18]Fierer N, Jackson JA, Vilgalys R, Jackson RB: Assessment of microbial community structure by use of taxon-specific quantitative PCR assay. Appl Envirn Microbiol 2005, 71:4117-4120.
• [19]Bacchetti de Gregoris T, Aldred N, Clare AS, Burgess JG: Improvement of phylum- and class-specific primers for real-time PCR quantification of bacterial taxa. J Microbiol Methods 2011, 86:351-356.
• [20]Brusetti L, Borin S, Mora D, Rizzi A, Raddadi N, Sorlini C, Daffonchio D: Usefulness of length heterogeneity-PCR for monitoring lactic acid bacteria succession during maize ensiling. FEMS Microbiol Ecol 2006, 56:154-164.
• [21]Suppiah J, Thimma JS, Cheah SH, Vadivelu J: Development and evaluation of polymerase chain reaction assay to detect Burkholderia genus and to differentiate the species in clinical specimens. FEMS Microbiol Lett 2010, 306:9-14.
• [22]Podolich O, Laschevskyy V, Ovcharenko L, Kozyrovska N, Pirttila AM: Methylobacterium sp. resides in unculturable state in potato tissues in vitro and becomes culturable after induction by Pseudomonas fluorescens IMGB163. J Appl Microbiol 2009, 106:728-737.
• [23]Yim MS, Yau YCW, Matlow A, So JS, Zou J, Flemming CA, Schraft H, Leung KT: A novel selective growth medium-PCR assay to isolate and detect Sphingomonas in environmental samples. J Microbiol Methods 2010, 82:19-27.
• [24]Vorwerk S, Martinez-Torres D, Forneck A: Pantoea agglomerans-associated bacteria in grape phylloxera (Daktulosphaira vitifoliae, Fitch). Agric For Entomol 2007, 9:57-64.
• [25]Constable FE, Gibb KS, Symons RH: Seasonal distribution of phytoplasmas in Australian grapevines. Plant Pathol 2003, 52:267-276.
• [26]Prezelj N, Nikolic P, Gruden K, Ravnikar M, Dermastia M: Spatiotemporal distribution of flavescence dorée phytoplasma in grapevine. Plant Pathol 2013, 62:760-766.
• [27]Romanazzi G, Musetti R, Marzachì C, Casati P: Induction of resistance in the control of phytoplasma diseases. Petria 2009, 19:113-129.
• [28]Goyer C, Dandie CE: Quantification of Microorganism Targeting Conserved Genes in Complex Environmental Samples Using Quantitative Polymerase Chain Reaction. In Quantitative Real-time PCR in Applied Microbiology. Edited by Filion M. Moncon: Caister Academic Press; 2012:87-109.
• [29]Bell CR, Dickie GA, Harvey WLG, Chan JWYF: Endophytic bacteria in grapevine. Can J Microbiol 1994, 41:46-53.
• [30]Williams KP, Gillespie JJ, Sobral BWS, Nordberg EK, Snyder EE, Shallom JM, Dickerman AW: Phylogeny of Gammaproteobacteria. J Bacteriol 2010, 192:2305-2314.
• [31]Mocali S, Bertelli E, Di Cello F, Mengoni A, Sfalanga A, Viliani F, Caciotti A, Tegli S, Surico G, Fani R: Fluctuation of bacteria isolated from elm tissues during different seasons and from different plant organs. Res Microbiol 2003, 154:105-114.
• [32]Araujo WL, Marcon J, Maccheroni W, Van Elsas JD, Van Vuurde JWL, Azevedo JL: Diversity of endophytic bacterial populations and their interaction with Xylella fastidiosa in citrus plants. Appl Environ Microbiol 2002, 68:4906-4914.
• [33]Reiter B, Pfeifer U, Schwab H, Sessitsch A: Response of endophytic bacterial communities in potato plants to infection with Erwinia carotovora subsp. atroseptica. Appl Environ Microbiol 2002, 68:2261-2268.
• [34]Van Loon CL: Plant responses to plant growth-promoting rhizobacteria. Eur J Plant Pathol 2007, 119:243-254.
• [35]Musetti R, Marabottini R, Badiani M, Martini M, Sanità di Toppi L, Borselli S, Borgo M, Osler R: On the role of H2O2 in the recovery of grapevine (Vitis vinifera cv Prosecco) from Flavescence doreé disease. Funct Plant Biol 2007, 34:754-758.
• [36]McSpadden Gardener BB, Weller DM: Changes in population of rhizosphere bacteria associated with take-all disease of wheat. Appl Environ Microbiol 2001, 67:4414-4425.
• [37]Yang C, Crowley DE, Menge JA: 16S rDNA fingerprinting of rhizosphere bacterial communities associated with healthy and Phytophthora infected avocado roots. FEMS Microbiol Ecol 2001, 35:129-136.
• [38]West ER, Cother EJ, Steel CC, Ash GJ: The characterization and diversity of bacterial endophytes of grapevine. Can J Microbiol 2010, 56:209-216.
• [39]Mills DK, Entry JA, Gillevet PM, Mathee K: Assessing microbial community diversity using amplicon length heterogeneity polymerase chain reaction. Soil Sci Soc Am J 2007, 71:572-578.
• [40]Sessitsch A, Reiter B, Pfeifer U, Wilhelm E: Cultivation- independent population of bacterial endophytes in three potato varieties based on eubacterial and Actinomycetes-specific PCR of 16S rRNA genes. FEMS Microbiol Ecol 2002, 39:23-32.
• [41]Dent KC, Stephen JR, Finch-Savage WE: Molecular profiling of microbial community associated with seeds of Beta vulgaris subsp. vulgaris (Sugar beet). J Microbiol Methods 2004, 56:17-26.
• [42]Compant S, Nowak J, Coenye T, Clément C, Ait Barka E: Diversity and occurrence of Burkholderia spp. in the natural environment. FEMS Microbiol Rev 2008, 32:607-626.
• [43]Ardanov P, Sessitsch A, Häggman H, Kozyrovska N, Pirttila AM: Methylobacterium-Induced endophyte community changes correspond with protection of plants against pathogen attack. PLoS One 2012, 7:e46802.
• [44]Vogel C, Innerebner G, Zingg J, Guder J, Vorholt JA: Forward genetic in planta screen for identification of plant-protective traits of Sphingomonas sp. strain Fr1 against Pseudomonas syringae DC3000. Appl Environ Microbiol 2012, 78:5529-5535.
• [45]Magnin-Robert M, Quantinet D, Couderchet M, Aziz A, Trotel-Aziz P: Differential induction of grapevine resistance and defense reactions against Botrytis cinerea by bacterial mixtures in vineyards. Biocontrol 2013, 58:117-131.